"Many are those who seek refuge in other countries, fleeing war, persecution and natural disasters, and while accepting them poses many problems, it is however a duty," said Benedict, speaking in Puglia at the shrine to Padre Pio, one of Italy's most popular saints.
The pope's comments come as Italy enforces tougher legislation to block foreign migrants from entering the country.
Rome and Tripoli recently implemented a controversial new policy which allows the Italian navy to intercept illegal migrants at sea and return them to Libya, from where they set off for Europe.
Rome's agreement with Tripoli to repatriate the migrants, many from sub-Saharan Africa, has been sharply criticised by rights groups including the UN High Commissioner for Refugees, as well as the Vatican, on grounds that genuine asylum seekers may be among them.
Libya is not a signatory to the UN refugee convention and the UNHCR has no access to immigration centres in the north African country.
The pope also addressed jobless youths, urging them not to lose hope amid the current economic gloom.
Speaking at a church which forms part of Padre Pio's shrine, Benedict told a group of young people "not to be discouraged".
"I am aware of the problems which are affecting you and which threaten to cast a shadow over the joys of being young," he told the group.
"I am referring, in particular, to the problem of unemployment which is hitting lots of young people, both male and female, of the Mezzogiorno (the south of Italy)."
The pope added: "The church will not abandon you. Don't abandon the church."
Italy's unemployment rate is rising as the country is buffeted by the global economic crisis.
It rose to 7.3 percent in the first quarter of this year from a revised figure of 7.0 in the last quarter of 2008, according to adjusted official data released Friday by national statistics body Istat.
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